From 15533e08dfdb28002c5fe9cb0925cd3d4242268c Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Wed, 7 Dec 2011 11:55:42 -0500 Subject: [PATCH] Fixed issue with RODWalker parallelization. Turns out that someone previously upped the declared size of a ROD shard to 100M bases, making each ROD shard larger than the size of chr20. Why didn't we see this in Stable? Because the ShardStrategy/ShardStrategyFactory mechanism was dutifully ignoring the shard size specification. When I rolled the ShardStrategy/ShardStrategyFactory mechanics back into the DataSources as part of the async I/O project, I inadvertently reenabled this specifier. --- .../src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 7cc8e9e29..d37116215 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -469,7 +469,7 @@ public class GenomeAnalysisEngine { throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName()); } else { - final int SHARD_SIZE = walker instanceof RodWalker ? 100000000 : 100000; + final int SHARD_SIZE = walker instanceof RodWalker ? 1000000 : 100000; if(intervals == null) return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE); else